If the two missing people are found to have died as a result of the explosion, the bombing would mark Eta's first fatal attack since a car bomb killed two policemen in the northern town of Sanguesa in May 2003.
The car bomb, which injured over 25 people, exploded on 30 December at Madrid's international airport.
Eta, the Basque separatist group, later claimed responsibility for the car bomb in a telephone call to the Spanish state radio.
The Spanish government has subsequently suspended dialogue with the group.
"I have decided to suspend all initiatives for dialogue with Eta," Jose Luis Rodriguez Zapatero, the prime minister, told a news conference.
Alfredo Perez Rubalcaba, the interior minister, earlier said the blast has "broken the ceasefire the Eta called on March 22".
On Saturday, Terminal Four at Barajas Airport was evacuated after a warning was telephoned to motorway rescue services in the Basque Country, state radio reported.
Eta had declared a ceasefire in March after 40 years of armed struggle for independence of the Basque Country in which it killed more than 800 people.
Zapatero announced in June that he would start a peace process with Eta.
However, the group said last month that it would break off contacts unless there was quick progress in separate talks over the future of the Basque Country.
Eta was founded in 1959 to fight for Basque self-determination and Spain's interior ministry estimates over 800 people have been killed by the group since their first attack in the 1960s.